Gene loci information

Transcript annotation

  • This transcript has been annotated as Endoplasmic reticulum chaperone BiP.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_3 g2685 g2685.t15 isoform g2685.t15 19712637 19714329
chr_3 g2685 g2685.t15 exon g2685.t15.exon1 19712637 19713361
chr_3 g2685 g2685.t15 cds g2685.t15.CDS1 19712638 19713361
chr_3 g2685 g2685.t15 exon g2685.t15.exon2 19713517 19713661
chr_3 g2685 g2685.t15 cds g2685.t15.CDS2 19713517 19713644
chr_3 g2685 g2685.t15 exon g2685.t15.exon3 19713960 19714329
chr_3 g2685 g2685.t15 TSS g2685.t15 NA NA
chr_3 g2685 g2685.t15 TTS g2685.t15 NA NA

Sequences

>g2685.t15 Gene=g2685 Length=1240
ATGAAAAGTTTGAATGGTTTGAATTTTACATATTACGTTAATTTTTAAATCAAAAATTTT
ATGTCATCCAAAATATGATGAAATATGACCAAGTTTCTCAATAAAACATCCTCTCAAATT
CAAAAATACTCTTTGAAATAGGTTGAAAATGGAACAAAAGAACACGTCAGTATAGAAAAG
AGAGATAGTATAAATTGTGAGCAATGAGACCAAATTTCAAGTCATTTCACTAAAAGGTTT
CACAGAGTAAAGACATCAAAAAAAAGATTGAGTAAAAAATTGAGTTATTTAAAGTGATTT
ATCTAGTGAAGTTAAGTAAATTTAATAATTTTGAATTATCAAATAAGAGTAGTTAAGCTA
TTAAAAGTAAGTAGAAACAAAATTAAAATGAGATTAACTCTATCATTCGTGGTCGTGGCG
GCATTCAGTGTGCTGGGAGTTCTTTCGAGCGAGGATAAGGATAAAAAAGATATTGGTACA
GTGATCGGTATCGATTTGGGAACGACATATTCATGTGTCGGAGTATATAAGAATGGACGT
GTAGAAATTATTGCAAATGATCAAGGAAATCGTATCACACCTTCATATGTGGCATTCACT
TCTGAAGGAGAACGATTGATTGGTGATGCAGCTAAAAATCAGCTCACAACAAATCCAGAA
AATACTGTGTTCGATGCTAAACGTCTAATTGGTCGTGAATGGAGTGACTCAGCTGTTCAA
CATGATATCAAATTTTTCCCATTCAAAGTTGTCGAGAAGAACTCAAAGCCACACATTGAA
GTGAAAACTCAACAAGGCAACAAAGTCTTCACACCTGAAGAAATTTCAGCTATGGTTCTT
GGAAAAATGAAAGAAACTGCTGAGGCATATTTGGGCAAAAAAGTTACGCACGCTGTTGTC
ACAGTTCCAGCTTATTTCAATGATGCTCAACGTCAAGCCACAAAAGATGCTGGTATCATC
TCTGGATTGAATGTTATGCGTATTATTAATGAACCTACTGCAGCAGCTATTGCATATGGG
CTTGATAAAAAAGACGGCGAAAAGAATGTTTTAGTATTCGATCTTGGTGGTGGTACATTC
GATGTCTCGCTTCTTACAATTGATAACGGTGTTTTCGAAGTTGTTGCCACAAATGGTGAT
ACTCACTTAGGAGGTGAAGATTTTGATCAACGTGTGATGGATCATTTCATTAAATTGTAC
AAGAAGAAGAAGGGCAAGGACATTCGTAAAGATAATCGCG

>g2685.t15 Gene=g2685 Length=284
MRLTLSFVVVAAFSVLGVLSSEDKDKKDIGTVIGIDLGTTYSCVGVYKNGRVEIIANDQG
NRITPSYVAFTSEGERLIGDAAKNQLTTNPENTVFDAKRLIGREWSDSAVQHDIKFFPFK
VVEKNSKPHIEVKTQQGNKVFTPEEISAMVLGKMKETAEAYLGKKVTHAVVTVPAYFNDA
QRQATKDAGIISGLNVMRIINEPTAAAIAYGLDKKDGEKNVLVFDLGGGTFDVSLLTIDN
GVFEVVATNGDTHLGGEDFDQRVMDHFIKLYKKKKGKDIRKDNR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g2685.t15 Gene3D G3DSA:3.30.420.40 - 32 210 1.7E-120
13 g2685.t15 Gene3D G3DSA:3.30.420.40 - 211 254 1.7E-120
12 g2685.t15 Gene3D G3DSA:3.90.640.10 Actin; Chain A 255 284 1.7E-120
2 g2685.t15 PANTHER PTHR19375 HEAT SHOCK PROTEIN 70KDA 18 284 6.7E-158
3 g2685.t15 PANTHER PTHR19375:SF380 ENDOPLASMIC RETICULUM CHAPERONE BIP 18 284 6.7E-158
6 g2685.t15 PRINTS PR00301 70kDa heat shock protein signature 31 44 1.0E-37
5 g2685.t15 PRINTS PR00301 70kDa heat shock protein signature 59 71 1.0E-37
7 g2685.t15 PRINTS PR00301 70kDa heat shock protein signature 82 90 1.0E-37
8 g2685.t15 PRINTS PR00301 70kDa heat shock protein signature 169 189 1.0E-37
4 g2685.t15 PRINTS PR00301 70kDa heat shock protein signature 229 239 1.0E-37
1 g2685.t15 Pfam PF00012 Hsp70 protein 32 284 3.6E-128
16 g2685.t15 Phobius SIGNAL_PEPTIDE Signal peptide region 1 20 -
17 g2685.t15 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
18 g2685.t15 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 16 -
19 g2685.t15 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 17 20 -
15 g2685.t15 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 21 284 -
20 g2685.t15 ProSitePatterns PS00297 Heat shock hsp70 proteins family signature 1. 35 42 -
21 g2685.t15 ProSitePatterns PS00329 Heat shock hsp70 proteins family signature 2. 223 236 -
10 g2685.t15 SUPERFAMILY SSF53067 Actin-like ATPase domain 30 214 5.01E-73
9 g2685.t15 SUPERFAMILY SSF53067 Actin-like ATPase domain 216 283 1.39E-21
11 g2685.t15 SignalP_EUK SignalP-noTM SignalP-noTM 1 20 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005524 ATP binding MF
GO:0016887 ATP hydrolysis activity MF

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below. There were no conditions that were differentially expressed